CC = gcc
CFLAGS = -O3 -Wall 
CFLAGS += -D_FILE_OFFSET_BITS=64
CFLAGS += -D_LARGEFILE_SOURCE
CFLAGS += -fno-exceptions
CFLAGS += -finline-functions
CFLAGS += -funroll-loops

all: clean sortReads blindSearch validateMatches
sortReads:
	$(CC) $(CFLAGS) sortReads.c utils.c -o sortReads
blindSearch:
	$(CC) $(CFLAGS) DIGEST_V2/search.c blindSearch.c utils.c -o blindSearch
validateMatches:
	$(CC) $(CFLAGS) DIGEST_V2/search.c validateMatches.c utils.c -o validateMatches
	
clean:  
	rm -f sortReads blindSearch validateMatches
